Water

The chemical formula of a single water molecule is H2O, meaning that it is composed of 2 hydrogen atoms and 1 oxygen atom. Oxygen is very
electronegative, or attractive to electrons. As a result, a water molecules electrons tend to spend more time near the oxygen atom than the hydrogen
atom. This gravitation of negatively-charged electrons towards the oxygen gives that region of the molecule a slight negative charge. The hydrogen
atoms, in contrast, have slightly positive charges. Water is thus a polar molecule. The weak interactions between positively and negatively charged
regions of individual water molecules are called hydrogen bonds. These bonds are very low energy and can thus easily break and form. These
interactions become stronger, however, when tens of thousands of water molecules are grouped together, as most will be hydrogen bonded to their
neighbours at any given moment. This leads us to the special properties of water, which are:
Cohesion
Because of the cumulative force of thousands of hydrogen bonds, water molecules tend to stick together. Water droplets hanging from the nozzle of a
hose are held together by these bonds. In addition, cohesion allows for the movement of water up through the body of a plant. Water molecules
evaporating from the leaves at the top of the plant are still connected to molecules just inside the leaf. When the evaporating molecules move away
from the plant and into the air, they gently tug their neighbours in the leaf with them. This second group of molecules pulls up a third group, a process
which continues all the way to the bottom of the plant. Imagine that water molecules are tiny balls linked by string: when you pull a clump of balls at
the top, the rest of the chain will follow.

Cohesion also raises waters surface tension, or the force needed to break the surface of the liquid. This phenomenon is also caused by hydrogen bonds,
and allows some small insects to run across water.

Resistance to Temperature Change

Chemically speaking, temperature is a measure of the average kinetic energy of a group of molecules. Kinetic energy describes the speed at which a
molecule is moving. When two objects touch, heat is transferred until their temperatures are equal. This is because the fast-moving molecules of one
surface bump into the slower-moving molecules of the other. These collisions make the slow molecules move a little faster and the fast ones a little
slower.

Water molecules are stuck together fairly tightly due to hydrogen bonds, which makes it harder to speed or slow their movement. For this reason, water
has a relatively high specific heat, which is a measure of the amount of energy it takes to raise the temperature of 1g of water by 1 Celsius.

Water also tends to cool by evaporating. Temperature is a measure of the average speed of a group of molecules: some will move faster and others
slower. The fastest molecules are most likely to break free from hydrogen bonds of the group and become a gas (which is the same as liquid water,
except the molecules are spaced farther apart), leaving the slower (i.e., cooler) molecules behind.
Ability to Dissolve Polar Substances
If you put a salt in a glass of water, the salt soon dissolves. Why? Salt is a polar compound composed of Na+ and CL- (sodium and chlorine) ions. When
placed in water, sodium and chlorine ions on the outside of the salt crystal are quickly surrounded by water molecules, which form weak polar
interactions using their positive or negative regions. Water molecules continue separating and encircling the component ions of the salt crystal, wearing
down the outermost layer until nothing remains. In this case, dissolved by water means that the components of the solute (dissolved substance) are
interacting via hydrogen bonds with the solvent (dissolving agent, such as water).

Acids and Bases

A solution (which is composed of solutes dissolved in a solvent) can be acidic or basic. High concentrations of hydrogen ions (H+) and hydroxide ions
(OH-) make a solution acidic or basic, respectively.

The amount of hydrogen or hydroxide ions in a solution is denoted using the pH scale. The more H+ ions there are in a solution, the lower the pH of
that solution. Distilled water has a pH of 7, which is the midpoint of the scale. This means that the solution has equal concentrations of H+ and OH- ions.
In addition, the pH scale is logarithmic, which means that each level is separated from its neighbours by a factor of ten. Thus, a solution with pH 5 is
ten times more acidic than pH 6, and ten times more basic than pH 4.
Organic Molecules
Organic molecules contain carbon, which is one of the most important elements for living things. Carbon needs 4 electrons to complete its outer shell,
and can thus form four bonds. The major organic molecules you need to know are:

Carbohydrates
Lipids
Nucleotides
Polypeptides

Carbohydrates:
Carbohydrates are composed of ring-shaped molecules such as glucose:
The above glucose molecule is also called a monosaccharide, as it is composed of only one molecule. The Latin prefix mono means one. When
you take two monomers and join them, a disaccharide is formed through dehydration synthesis, shown below:

This disaccharide forms as a result:

Monosaccharides and disaccharides are known as sugars, which provide your body with a quick burst of energy. Long chains of glucose molecules are
called polysaccharides (poly for many) or starch, and are used to store energy long-term. A polysaccharide is formed by dozens or hundreds of
dehydration synthesis reactions. The reaction that breaks the bond between glucose molecules is called hydrolysis.

There are a few important groups of polysaccharides that you should know:

Starches long, linear chains of glucose used to store energy in plants

Glycogen similar to starch, but with a branched structure. This makes the molecule less compact but also creates multiple ending points. An
enzyme can detach glucose molecules from any one of glycogens dozens of end points, allowing for much quicker access to energy (with
starch, there are only two end points, so only two glucose molecules can be detached at a time). Glycogen is used to store energy in animals,
and makes up the short-term energy reserves in your liver.
Cellulose a linear chain like starch, but its glucose molecules are connected to each other by a different bond (which humans cant digest).
Cell walls in plants are composed of cellulose.
Lipids
Lipid is the scientific term for fats. Fats have two components: fatty acids and a glycerol. If a fat only has single bonds, then the fat is said to be
saturated, meaning that is has as many hydrogen atoms as possible. Fats with double bonds have a more bent structure and are unsaturated.
Phospholipids are another type of lipid that makes up the cell membrane. Phospholipids have a hydrophilic head (which is polar and can form hydrogen
bonds with water) and a hydrophobic tail. The head region contains a phosphate group, while the tail is composed of a pair of fatty acids.

Cholesterol Molecule
Finally, steroids are also included in the lipid category. The most important steroid is cholesterol, which is used as the foundation for many other
steroids. Steroids all have four fused carbon-based rings, which is useful if you need to identify them.

Nucleotides
DNA and RNA are molecules that carry heredity information inside a cell. Individual DNA and RNA nucleotides are almost exactly the same, except
RNA nucleotides has a single extra oxygen atom. Well discuss DNA and RNA more in depth later. For now, just remember that nucleotides have
three parts:

A phosphate group
A five-carbon sugar
 A nitrogen base
Proteins
Proteins are composed of individual amino acids, which also have three parts:

An amino group
A carboxyl group
A carbon bonded to a hydrogen atom and a functional group (different for each amino acid).

Individual amino acids can be connected by a dehydration reaction, which forms peptide bonds
Proteins have four levels of structure:

The primary structure of a protein is a simple chain of amino acids

The secondary structure often contains repeating patterns: either helixes or sheets. These structures are created by the hydrogen bonds that
form between groups of amino acids.
Tertiary structure is formed when the different secondary structures cluster together, forming hydrogen bonds with each other. The tertiary
structure of a protein is further fixed by the formation of covalent bonds called disulfide bridges.
The quaternary structure of a protein is made up of tertiary structure-level subunits.

Proteins fold spontaneously, moving to the lowest potential energy position possible. Bonds form, structures come together or separate all in obedience
to the laws of thermodynamics.

Enzymes
While proteins can do many tasks, one of the most important is their role as enzymes. Enzymes speed the rate of a reaction without changing the
outcome. Enzymes bring the two reactants close together, forcing them to collide and lowering the activation energy required for the reaction.
Enzymes have specific regions, called active sites, where substrates (the reactants) can bind. Active sites have a very specific shape, and can only bind
the intended substrate or something very similar. Also, enzymes tend to change their shape slightly to fit incoming substrates, which is called induced
fit.
Human enzymes generally work best at a pH of 7 (neutral) and at 37C (body temperature).

Enzyme Regulation
There are a few types of enzyme regulation:

Allosteric Regulation Allosteric regulators bind to sites on a protein, changing its shape. These changes can either activate or deactivate the
protein.
Feedback Inhibition A mechanism used to prevent overproduction: high concentrations of the end result of a reaction inhibit proteins that
start the reaction.
Competitive Inhibition Adding molecules that are similar enough to a proteins substrate to bind to its active site slows the rate of the reaction,
as the protein doesnt bind the right substrates all the time.
 Coenzymes and Cofactors We know them as vitamins and minerals. These molecules also bind to enzymes and turn them on or off.

Energy for Reactions

Proteins generally catalyze bond formation, which requires an investment of energy. This energy can come from ATP.